NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM397815 Query DataSets for GSM397815
Status Public on Jul 31, 2010
Title Blood-Ctrl-0909-rep1
Sample type genomic
 
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 3 / Father
twin #: NA
twin info: NA
gender: M
phenotype: Ctrl
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from leukocytes using the phenol chloroform method or Qiamp blood kits (Qiagen Pty Ltd, Doncaster, Vic, Australia), hair using the phenol chloroform method, and from sperm using Pure Sperm 100 kits (Nidacom, Gothenburg, Sweden).
Label biotin
Label protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia), Affymetrix dsDNA terminal label.
 
Hybridization protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Scan protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Description Affy 6.0 Ctrl Blood
Data processing Data processed using Affymetrix Command Console software and Affymetrix Genotyping Console 3.0.2 software using the Birdseed version 2 algorithm and default settings.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
 
Submission date Apr 25, 2009
Last update date Jun 26, 2012
Contact name Roger Pamphlett
Organization name University of Sydney
Street address Blackburn Bld
City University of Sydney
ZIP/Postal code 2006
Country Australia
 
Platform ID GPL6801
Series (1)
GSE15826 Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE A value in the range [0,1] with lower values corresponding to greater confidence
FORCED CALL This value is the genotyping call that would be made if the calling algorithm were tuned to the least stringency. Providing this value allows for determining what the calls would have been at a stringency different to that applied to the calls in the second field, without having to re-run the genotyping algorithm
SIGNAL A Summarized signal A
SIGNAL B Summarized signal B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.005274 BB 543.055298 3761.914795
SNP_A-1967418 BB 0.001772 BB 245.808075 769.001648
SNP_A-1969580 BB 0.014355 BB 1130.959229 4969.781250
SNP_A-4263484 AB 0.011585 AB 1848.818115 1020.693298
SNP_A-1978185 AA 0.004885 AA 928.429810 327.657501
SNP_A-4264431 AB 0.006091 AB 1486.070801 1067.462646
SNP_A-1980898 AB 0.055942 AB 908.941162 626.563965
SNP_A-1983139 AA 0.031565 AA 2626.100098 645.160400
SNP_A-4265735 AB 0.003002 AB 1578.438110 1666.653564
SNP_A-1995832 BB 0.002589 BB 522.308777 2041.513672
SNP_A-1995893 BB 0.007492 BB 505.269684 2589.261719
SNP_A-1997689 BB 0.002550 BB 632.099915 3989.504639
SNP_A-1997709 AA 0.008495 AA 1192.517212 209.278549
SNP_A-1997896 AB 0.006151 AB 1232.819824 1544.249390
SNP_A-1997922 AB 0.002720 AB 819.397339 712.274292
SNP_A-2000230 AA 0.002895 AA 2480.604248 1095.856812
SNP_A-2000332 AA 0.002415 AA 3830.137939 916.890991
SNP_A-2000337 AA 0.001590 AA 1707.153931 251.253479
SNP_A-2000342 AA 0.001422 AA 4378.240234 1038.171631
SNP_A-4268173 AB 0.003136 AB 893.020386 657.262817

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.




Supplementary file Size Download File type/resource
GSM397815.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM397815.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap